Neel
Bioinformatics Beginner
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Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1000 days ago
https://github.com/KamilSJaron/smudgeplot
This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.
Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:
